Engineering on a Grand Scale with the Smallest of the Small

Microbial life engineered most of what underpins life on earth, yet it’s only recently that engineers have started viewing the world of microbes as a vast and unexplored toolbox of highly efficient chemical processes.

Microbes living on or in the human body are so numerous that they actually outnumber our own cells, and many perform functions so critical to health that we literally couldn’t survive without them. The same can be said of microbial life in our natural environment, where clean water and oxygen are just two essentials that come largely courtesy of microorganisms.

Yet, while microbes are such heavy lifters in our natural environment, their role in our built environment is limited.

But that’s changing, and various members of the Colorado School of Mines community are contributing to the transformation as they look beyond wastewater treatment, where they have been used for generations, and explore new ways to put microbes to work on biofuels, plastics, gas stimulation, industrial cleanup and even mining.

“Virtually every surface is covered in microbes, and they are all performing some sort of service that we take for granted,” says John Spear MS ’94, PhD ’99, an associate professor of civil and environmental engineering at Mines. “My job is to look at life in any environment and ask, ‘Who is there? What are they doing? And how can we use what they are doing to benefit humans?'”

Put a corroded steel pipe or a piece of rotting lumber in front of most people and they see the nuisance impacts of microorganisms; Spear sees a world of opportunity.

Since taking his teaching position at Mines in 2005, Spear has joined a growing number of scientists on campus and beyond who are working to, as he puts it, ‘connect the dots’ between microbiology and mining, metallurgy, and petroleum and chemical engineering. For years a small group of applied scientists have contended that with a better understanding of microbes, we can extract minerals more efficiently, clean up hazardous waste more economically, develop cheaper biofuels and plastics, and much more.

Now, with fuel prices on the rise, a warming planet, and water quality increasingly threatened, more people are listening, funding is more forthcoming and the idea of enlisting microscopic organisms to engineer our world in creative new ways is catching on.

“Microbiology is an extremely exciting field right now,” says Spear. “In the next 10 years, it could enable us to solve some really complex problems.”

Matthew Posewitz and collaborators are working to develop more productive strains of algae for biofuel production.

Green crude

As far back as the 1950s, scientists have studied the potential of cultivating algae as a source of oil. Like tiny floating factories, microalgae use sunlight and carbon dioxide to manufacture fats, which they pack away as a food store. Since they generally grow swiftly (some able to double their weight in just a few hours if conditions are right) and many strains can live in brackish water, they could be cultivated in environments where they don’t compete for water or land with food crops. They’re also super-efficient, generating 10 to 30 times more oil per acre than other biofuel oil crops such as soybeans, according to a report by the National Renewable Energy Laboratories.

In 1978, the U.S. Department of Energy launched an ambitious Aquatic Species Program at NREL to explore feeding carbon dioxide emissions from coal-fired power plants through tanks of algae. With annual funding of $2.75 million, scientists gathered 300 hungry algae strains to study, but when oil prices bottomed out, so did interest in the program, which died in 1996.

Today, algae are making a comeback. “There’s an incredible amount of interest in this right now,” says Matthew Posewitz, an assistant professor of chemistry and geochemistry at Mines, who has been studying algal biofuels for 12 years. “We have made a lot of progress in the last few years.” Posewitz points out that most of the oil we pump out of the ground originated from unicellular microorganisms that geological pressure, heat and time have converted into oil. “Essentially, we are trying to do that in real time,” he explains.

A key challenge with algae, Posewitz points out, is that they naturally prefer to make long-chain fatty acids, but short-chain fatty acids work better at lifting a jet or keeping a school bus running in mid-winter temperatures. It can also be exceedingly costly to squeeze the oil out of plump, well-fed algae. (In 1996, according to NREL, the price of oil hit $20 a barrel, while the price of algal fuel was estimated to be four times that.)

“The big issue has always been that fossil fuel is extremely inexpensive, and it’s hard for biology to compete with that,” Posewitz says, but they are making headway.

With several million dollars in new funding from the U.S. Air Force, the Department of Energy, the National Science Foundation, ConocoPhillips and others, Posewitz and his colleagues have collected more than 150 prolific strains of wild algae in vats that line his lab. Their aim: to develop a strain, either through genetic manipulation or changes in inputs such as food source and sunlight levels, that quickly stores short-chain lipids and liberates them easily.

In fact, he and two scientists in his lab, post-doc Randor Radakovits and graduate student Robert Jinkerson, just published a paper in Nature Communications that lays out a blueprint for a genetically modified alga that splices traits from several other organisms into the species Nannochloropis gaditana, which is naturally a great lipid producer.

“We have a great wild critter and now we are going to make it even better,” says Posewitz, explaining that it not only can thrive in saltwater, but will also produce short-chain fatty acids and isoprenes that are better fuel molecules.

The blueprint is based on their own research and on the work of numerous labs around the world; it’s an uber-alga incorporating qualities cherry-picked from a robust body of knowledge that Posewitz believes is reaching critical mass. “We are at a watershed moment in this field,” he says.

NREL has also revived its algal fuels program and is working with a company called Algenol to expedite commercialization. It could be decades before algal fuels rival fossil fuel in price, Posewitz says, but for those willing to pay a premium for a vehicle that runs on algae-generated biofuel, that option might soon be a lot more available.

Gas farming

Meanwhile, Golden-based Luca Technologies (at which Spear serves as scientific advisor) is working on another new ‘real time’ fuel option, one that encourages native microbes, called methanogens, to multiply and gobble underground coal deposits, converting them to methane for use as natural gas.

“Traditional oil and gas is more a hunter-gatherer approach,” explains Luca CEO Bob Cavnar, who describes his company as farmers. “We are actually growing gas slowly by reactivating and feeding these methanogens.”

Thus far, the company has purchased about 160 underground deposits in Wyoming (mostly uneconomic coal-bed methane wells that were shut down), which they are infusing with nutrients to wake up the naturally occurring coal-eating microbes and encouraging them to multiply and produce gas. However, the approach is so new that they have to clear some regulatory hurdles before they can start harvesting the gas. “We think this is a huge opportunity to get natural gas into the market,” Cavnar says.

Plastic bugs

Chemical engineering professor John Dorgan has a different end product in mind when he sees a teeming vat of bacteria: plastic.

Since 1993, Dorgan has been pioneering the field of bioplastics, which rely on microorganisms to chew up plant sugars, like those in corn, and spit out plastic precursors. “When they are fat and happy, they grow polyester, but when they are lean and stressed, they excrete it and use it as an energy source,” explains Dorgan. Back when he entered the field, few people had heard of bioplastics; today they are widely used in food packaging, plastic utensils and clothing.

Now Dorgan is seeking to improve the manufacturing process by figuring out how to use cellulose from sources like corncobs and stalks to feed bacteria, rather than just relying on edible corn sugars.

“You could redesign our farm harvesting machines and instead of throwing out the non-edible parts of the corn, you could collect them and use them as a valuable source of fermentable sugars for plastic,” he says. “It’s a readily available resource that does not compete with the food supply.”

His research is particularly focused on finding or engineering the appropriate microorganism for the job, one that can chew through intractable cellulose and pack on plastic. Will the day come when our car parts and carpets can be made from bacteria-derived plastic? Absolutely, says Dorgan.

“This field is moving quite rapidly,” he says. “I have no doubt in my mind that within 50 years we will be able to make whatever plastic we want out of renewable resources.”

Microbes to the rescue

Microorganisms are also playing an increasingly important role in cleaning up industrial waste.

“Instead of hogging it out of the ground and hauling it off to a landfill, we can treat contamination in place,” says Scott Noland ’87, who graduated from Mines with a degree in chemical and petroleum engineering. In 2002 Noland launched Remediation Products Inc., a Golden-based company that populates the pores of activated carbon with 25 species of hydrocarbon-hungry microorganisms for injection into subsurface plumes of petroleum or other pollutants.

For decades, environmental engineers have relied on naturally occurring resident bacteria to help with in-situ cleanup. The problem: It’s hard to generate enough bacteria to spread out and make contact with all the contaminant compounds, so it often takes a long time. Noland says his system delivers a huge population of just the right bacteria straight to the food source, the hydrocarbon, making short work of the cleanup. “Our product can clean up sites overnight,” claims Noland, recalling a Kentucky gas station owner who spent $730,000 over eight years on other cleanup measures before hiring RPI. Six months later he received a ‘no further action needed’ declaration from the state, having spent an additional $180,000.

Hydrocarbons aren’t the only problems microorganisms can tackle.

Based in Highlands Ranch, Colo., ARCADIS has stimulated native microorganisms at hundreds of sites across the United States, South America and Europe to clean up contaminants like hexavalent chromium, chlorinated solvents and explosives.

“The field is evolving as we develop approaches that incorporate hydrogeology, geochemistry, microbiology, engineering and other specialties to more effectively treat a broader array of contaminants,” says ARCADIS scientist Richard Murphy MS ’95, PhD ’00, whose degrees are in environmental science and engineering.

Mining with microbes

When it comes to mining, microorganisms have played a critical role for more than a century, since early biohydrometallurgists at the Rio Tinto mines in southwestern Spain first began piling up heaps of low-grade ore and leaving them to biodegrade over years, liberating inherent copper.

In the 1980s Mines graduate James Sharp ’61 took this process a step further, exploring the idea of boosting production of specific bacteria at mining sites to hasten the processing of low-grade ore. The idea grew out of his own frustration with a silver-bearing manganese oxide deposit he owned in the mountains of Colorado. It didn’t make economic or environmental sense to use leaching processes, which rely on cyanide and other chemicals, but he didn’t want to walk away.

“I can vividly remember him coming into the office and throwing around this idea of using bacteria to increase recovery of precious metals,” recalls Karen Oden, who worked with Sharp as a graduate student in Arizona in the 1980s. “It was definitely a new idea at the time.”

Over the course of three years, Sharp and Oden identified Bacillus strains that worked particularly well to break down the manganese lattice and liberate silver. Sharp, who died in 1998, ultimately founded the company MBX Systems, which held six patents and was later sold to other corporations that enhanced the biohydrometallurgical technologies.

Today, mining companies across the globe put armies of microorganisms to work liberating valuable metals from ores. “One-third of the copper we produce comes courtesy of three strains of bacteria,” says Harry ‘Red’ Conger ’77, president of the Americas division of Freeport-McMoRan Copper and Gold, the second largest copper producer in the world.

Engineering the future with microbiology

Ultimately, Spear believes microorganisms will play a much larger role in the engineering of our built environment. In his lab right now, he’s working with students on how to remove uranium from contaminated groundwater, turn wastewater into electricity, and prevent microorganisms from degrading underground fuel and sewer pipes. He also continues to look at various ways the extreme biology of microorganisms living in geothermal hot springs can be put to work.

He believes there are plenty more problems that biology can help solve, and he’s always on the lookout for opportunities to bring them to light. “With more connectivity, we can solve bigger, more complex problems,” he says. Often, the answers to those problems may be, literally, right before our eyes.

“Life has been around on this planet for about 4 billion years. That is 4 billion years of evolution to optimize processes,” Spear says. “If nature has already done it, why do we need to re-engineer it? We should look for solutions in nature first and capitalize on her processes.”